# CLI

```{toctree}
:hidden: true
:maxdepth: 1

scan
anno
generator
evaluate
refine
identity
```

This section documents the command-line interface (CLI) subcommands provided by VAMPIRE.

::::{grid} 1
:gutter: 2

:::{grid-item-card} `scan`
:link: scan
:link-type: doc
Scan sequences for tandem repeat region annotation.
:::

:::{grid-item-card} `anno`
:link: anno
:link-type: doc
Annotate single tandem repeat locus across population.
:::

:::{grid-item-card} `generator`
:link: generator
:link-type: doc
Generate synthetic tandem repeat sequences for benchmarking.
:::

:::{grid-item-card} `evaluate`
:link: evaluate
:link-type: doc
Evaluate and compare annotation results against real sequences.
:::

:::{grid-item-card} `refine`
:link: refine
:link-type: doc
Refine motif annotation.
:::

:::{grid-item-card} `identity`
:link: identity
:link-type: doc
Calculate identify matrix across repeat units.
:::

::::